Improved cleanTheMess fucntion esgemme.py

esgemme.py

@@ -286,35 +286,48 @@ def launchPred(prot,inAli,mutFile, normWeightMode, alphabet):
 # Remove temporary files
 def cleanTheMess(prot,bFile,fFile, chainID):
 
-	if bFile!='':
-		if bFile!=prot+"_"+chainID+".psiblast":
-			os.remove(prot+"_"+chainID+".psiblast")
-	else:
-		if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
-			os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
-	if fFile!='':
-		if fFile!=prot+"_"+chainID+".fasta":
-			if os.path.isfile(prot+"_"+chainID+".fasta"):
-				os.remove(prot+"_"+chainID+".fasta")		
-#	if os.path.isfile(prot+"/"+prot+"_jet.res"):
-#		os.rename(prot+"/"+prot+"_jet.res",prot+"_jet.res")
-#	os.remove(prot+".pdb")
+    if bFile!='':
+        if bFile!=prot+"_"+chainID+".psiblast":
+            os.remove(prot+"_"+chainID+".psiblast")
+    else:
+        if os.path.isfile(prot+"/"+prot+"_"+chainID+".psiblast"):
+            os.rename(prot+"/"+prot+"_"+chainID+".psiblast",prot+"_"+chainID+".psiblast")
+    if fFile!='':
+        if fFile!=prot+"_"+chainID+".fasta":
+            if os.path.isfile(prot+"_"+chainID+".fasta"):
+                os.remove(prot+"_"+chainID+".fasta")		
+    if os.path.isfile(prot+"_jet.res"):
+        os.remove(prot+"_jet.res")
+    if os.path.isfile(prot+".pdb"):
+        os.remove(prot+".pdb")
 	
 	# Get all files with suffix nwk
-	treefiles = glob.glob('*.nwk')
-
-	# Iterate over the list of files and remove individually
-	for file in treefiles:
-		os.remove(file)
-
-	dir_name = prot+"/"
-	if os.path.isdir(dir_name):
-		for f in os.listdir(dir_name): 
-			f_path = os.path.join(dir_name, f)
-			if os.path.isfile(f_path):
-				os.remove(f_path)
-		os.rmdir(dir_name)
+    treefiles = glob.glob('*.nwk')
+
+    # Iterate over the list of files and remove individually
+    for file in treefiles:
+        os.remove(file)
+
+    dir_name = prot+"/"
+    if os.path.isdir(dir_name):
+        for f in os.listdir(dir_name): 
+            f_path = os.path.join(dir_name, f)
+            if os.path.isfile(f_path):
+                os.remove(f_path)
+        os.rmdir(dir_name)
+
+    if os.path.isfile("bin1.fasta"):
+        os.remove("bin1.fasta")
+        os.remove("bin2.fasta")
+        os.remove("bin3.fasta")
+        os.remove("bin4.fasta")
+    
+    if os.path.isfile("caracTest.dat"):
+        os.remove("caracTest.dat")
 
+    if os.path.isfile("default.conf"):
+        os.remove("default.conf")
+    
 ###############################################################################
 def rankSortProteinData(dataArray, inverted=True):
     """